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The heterogeneous nature of both groundwater discharge to a lake (inflow) and nitrate concentrations in groundwater can lead to significant errors in calculations of nutrient loading. Therefore, an integrated approach, combining groundwater flow and transport modelling with observed nitrate and ammonium groundwater concentrations, was used to estimate nitrate loading from a catchment via groundwater to an oligotrophic flow-through lake (Lake Hampen, Denmark). The transport model was calibrated against three vertical nitrate profiles from multi-level wells and 17 shallow wells bordering a crop field near the lake. Nitrate concentrations in groundwater discharging to the lake from the crop field were on average 70 times higher than in groundwater from forested areas. The crop field was responsible for 96% of the total nitrate loading (16.2 t NO3 /year) to the lake even though the field only covered 4.5% of the catchment area. Consequently, a small change in land use in the catchment will have a large effect on the lake nutrient balance and possible lake restoration. The study is the first known attempt to estimate the decrease of nitrate loading via groundwater to a seepage lake when an identified catchment source (a crop field) is removed., (© 2014, National GroundWater Association.)